Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: G54V1

Calculation Name: 1WDZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UQB8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 231
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2296050.716054
FMO2-HF: Nuclear repulsion 2202623.377811
FMO2-HF: Total energy -93427.338243
FMO2-MP2: Total energy -93697.788307


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-2.1540.6650.069-1.262-1.6250.006
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.016
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A4SER00.006-0.0183.751-0.8210.710-0.002-0.785-0.7450.003
4A5ARG10.9900.9424.5581.0141.103-0.001-0.011-0.0760.000
5A6SER0-0.024-0.0496.6740.2410.2410.0000.0000.0000.000
6A7GLU-1-0.812-0.8723.5374.5585.2880.072-0.363-0.4380.003
7A8GLU-1-0.975-0.9874.057-1.783-1.3140.000-0.103-0.3660.000
8A9MET00.0220.0325.710-0.446-0.4460.0000.0000.0000.000
9A10HIS00.0290.0538.881-0.384-0.3840.0000.0000.0000.000
10A11ARG10.8580.9015.995-3.861-3.8610.0000.0000.0000.000
11A12LEU00.0130.0239.012-0.308-0.3080.0000.0000.0000.000
12A13THR0-0.004-0.00511.288-0.165-0.1650.0000.0000.0000.000
13A14GLU-1-0.863-0.92810.9491.2851.2850.0000.0000.0000.000
14A15ASN0-0.042-0.03610.715-0.213-0.2130.0000.0000.0000.000
15A16VAL00.0150.03914.036-0.084-0.0840.0000.0000.0000.000
16A17TYR00.022-0.00616.825-0.056-0.0560.0000.0000.0000.000
17A18LYS10.8100.90116.524-0.478-0.4780.0000.0000.0000.000
18A19THR00.0360.00817.079-0.051-0.0510.0000.0000.0000.000
19A20ILE0-0.025-0.01619.605-0.039-0.0390.0000.0000.0000.000
20A21MET0-0.054-0.02020.643-0.030-0.0300.0000.0000.0000.000
21A22GLU-1-0.835-0.91120.0190.3300.3300.0000.0000.0000.000
22A23GLN00.0030.00420.181-0.004-0.0040.0000.0000.0000.000
23A24PHE0-0.0240.01523.862-0.019-0.0190.0000.0000.0000.000
24A25ASN00.018-0.02125.764-0.026-0.0260.0000.0000.0000.000
25A26PRO0-0.033-0.01326.426-0.014-0.0140.0000.0000.0000.000
26A27SER0-0.004-0.01327.265-0.016-0.0160.0000.0000.0000.000
27A28LEU0-0.016-0.00229.864-0.012-0.0120.0000.0000.0000.000
28A29ARG10.8740.92231.803-0.143-0.1430.0000.0000.0000.000
29A30ASN00.0130.01233.129-0.008-0.0080.0000.0000.0000.000
30A31PHE0-0.011-0.00133.990-0.007-0.0070.0000.0000.0000.000
31A32ILE00.0170.00735.113-0.006-0.0060.0000.0000.0000.000
32A33ALA0-0.0010.00637.634-0.005-0.0050.0000.0000.0000.000
33A34MET00.001-0.00338.267-0.006-0.0060.0000.0000.0000.000
34A35GLY00.0240.01439.815-0.005-0.0050.0000.0000.0000.000
35A36LYS10.8840.90341.571-0.071-0.0710.0000.0000.0000.000
36A37ASN0-0.0120.00242.520-0.002-0.0020.0000.0000.0000.000
37A38TYR0-0.003-0.00244.378-0.003-0.0030.0000.0000.0000.000
38A39GLU-1-0.837-0.92045.7520.0500.0500.0000.0000.0000.000
39A40LYS10.8190.88846.800-0.053-0.0530.0000.0000.0000.000
40A41ALA00.0040.01249.233-0.002-0.0020.0000.0000.0000.000
41A42LEU00.0120.00548.477-0.002-0.0020.0000.0000.0000.000
42A43ALA00.0090.00451.867-0.001-0.0010.0000.0000.0000.000
43A44GLY00.0040.00553.725-0.001-0.0010.0000.0000.0000.000
44A45VAL0-0.029-0.01554.359-0.002-0.0020.0000.0000.0000.000
45A46THR0-0.007-0.03356.088-0.002-0.0020.0000.0000.0000.000
46A47TYR0-0.049-0.01557.943-0.001-0.0010.0000.0000.0000.000
47A48ALA00.0160.00159.741-0.001-0.0010.0000.0000.0000.000
48A49ALA0-0.015-0.00660.202-0.001-0.0010.0000.0000.0000.000
49A50LYS10.8160.91059.913-0.027-0.0270.0000.0000.0000.000
50A51GLY00.0960.05264.659-0.001-0.0010.0000.0000.0000.000
51A52TYR0-0.035-0.02264.627-0.001-0.0010.0000.0000.0000.000
52A53PHE0-0.007-0.00666.327-0.001-0.0010.0000.0000.0000.000
53A54ASP-1-0.865-0.93567.9520.0180.0180.0000.0000.0000.000
54A55ALA0-0.042-0.01870.099-0.001-0.0010.0000.0000.0000.000
55A56LEU0-0.011-0.00967.975-0.001-0.0010.0000.0000.0000.000
56A57VAL00.0150.01071.593-0.001-0.0010.0000.0000.0000.000
57A58LYS10.8310.91573.954-0.012-0.0120.0000.0000.0000.000
58A59MET0-0.016-0.01874.720-0.001-0.0010.0000.0000.0000.000
59A60GLY00.0310.01675.896-0.001-0.0010.0000.0000.0000.000
60A61GLU-1-0.909-0.94877.2630.0120.0120.0000.0000.0000.000
61A62LEU00.002-0.00179.2370.0000.0000.0000.0000.0000.000
62A63ALA00.0110.01979.794-0.001-0.0010.0000.0000.0000.000
63A64SER00.0030.00981.4780.0000.0000.0000.0000.0000.000
64A65GLU-1-0.913-0.96083.0910.0100.0100.0000.0000.0000.000
65A66SER0-0.081-0.04384.8130.0000.0000.0000.0000.0000.000
66A67GLN0-0.019-0.04186.7210.0000.0000.0000.0000.0000.000
67A68GLY00.0120.00488.0390.0000.0000.0000.0000.0000.000
68A69SER0-0.031-0.01582.9080.0000.0000.0000.0000.0000.000
69A70LYS10.9350.99082.532-0.007-0.0070.0000.0000.0000.000
70A71GLU-1-0.836-0.91681.4440.0060.0060.0000.0000.0000.000
71A72LEU0-0.009-0.01878.1590.0000.0000.0000.0000.0000.000
72A73GLY00.0280.01977.3310.0000.0000.0000.0000.0000.000
73A74ASP-1-0.898-0.94976.8370.0080.0080.0000.0000.0000.000
74A75VAL0-0.049-0.01973.5750.0000.0000.0000.0000.0000.000
75A76LEU0-0.0050.00172.9110.0000.0000.0000.0000.0000.000
76A77PHE00.0400.01472.1430.0010.0010.0000.0000.0000.000
77A78GLN0-0.018-0.00671.3110.0010.0010.0000.0000.0000.000
78A79MET0-0.031-0.00568.4420.0000.0000.0000.0000.0000.000
79A80ALA00.0330.02367.3540.0010.0010.0000.0000.0000.000
80A81GLU-1-0.789-0.86867.2500.0160.0160.0000.0000.0000.000
81A82VAL0-0.017-0.00363.7800.0010.0010.0000.0000.0000.000
82A83HIS0-0.033-0.01962.1260.0000.0000.0000.0000.0000.000
83A84ARG10.8380.89562.363-0.016-0.0160.0000.0000.0000.000
84A85GLN0-0.076-0.05062.3360.0010.0010.0000.0000.0000.000
85A86ILE00.0100.00157.9150.0010.0010.0000.0000.0000.000
86A87GLN00.0450.01457.9130.0020.0020.0000.0000.0000.000
87A88ASN0-0.004-0.01457.8150.0010.0010.0000.0000.0000.000
88A89GLN0-0.037-0.01855.9400.0010.0010.0000.0000.0000.000
89A90LEU00.0140.01452.1370.0010.0010.0000.0000.0000.000
90A91GLU-1-0.797-0.86053.1280.0300.0300.0000.0000.0000.000
91A92GLU-1-0.838-0.89353.1850.0330.0330.0000.0000.0000.000
92A93MET0-0.0220.01448.2660.0030.0030.0000.0000.0000.000
93A94LEU00.0340.02248.6380.0030.0030.0000.0000.0000.000
94A95LYS10.8340.89948.635-0.031-0.0310.0000.0000.0000.000
95A96SER0-0.053-0.03746.8270.0030.0030.0000.0000.0000.000
96A97PHE00.007-0.00441.8660.0040.0040.0000.0000.0000.000
97A98HIS00.0700.04243.7910.0040.0040.0000.0000.0000.000
98A99ASN0-0.057-0.03944.4650.0030.0030.0000.0000.0000.000
99A100GLU-1-0.870-0.93142.9620.0470.0470.0000.0000.0000.000
100A101LEU0-0.018-0.01137.7060.0040.0040.0000.0000.0000.000
101A102LEU0-0.036-0.00239.5640.0060.0060.0000.0000.0000.000
102A103THR00.0470.01439.8820.0060.0060.0000.0000.0000.000
103A104GLN0-0.021-0.01238.7870.0080.0080.0000.0000.0000.000
104A105LEU0-0.018-0.01634.1550.0070.0070.0000.0000.0000.000
105A106GLU-1-0.804-0.89335.5350.0820.0820.0000.0000.0000.000
106A107GLN00.0210.01036.5840.0080.0080.0000.0000.0000.000
107A108LYS10.8340.93533.364-0.085-0.0850.0000.0000.0000.000
108A109VAL00.0110.00731.1590.0110.0110.0000.0000.0000.000
109A110GLU-1-0.958-0.96132.3370.1230.1230.0000.0000.0000.000
110A111LEU00.015-0.00633.1190.0090.0090.0000.0000.0000.000
111A112ASP-1-0.758-0.82228.1330.2020.2020.0000.0000.0000.000
112A113SER00.0550.00926.4310.0130.0130.0000.0000.0000.000
113A114ARG10.9360.97826.290-0.147-0.1470.0000.0000.0000.000
114A115TYR00.0160.00727.4900.0140.0140.0000.0000.0000.000
115A116LEU00.0230.01823.1080.0210.0210.0000.0000.0000.000
116A117SER00.0220.00922.6670.0470.0470.0000.0000.0000.000
117A118ALA0-0.053-0.02522.9910.0320.0320.0000.0000.0000.000
118A119ALA0-0.0060.00023.1470.0200.0200.0000.0000.0000.000
119A120LEU00.0340.02716.1850.0290.0290.0000.0000.0000.000
120A121LYS10.9860.99119.055-0.318-0.3180.0000.0000.0000.000
121A122LYS10.8500.90820.802-0.293-0.2930.0000.0000.0000.000
122A123TYR00.031-0.00112.903-0.029-0.0290.0000.0000.0000.000
123A124GLN0-0.018-0.05114.278-0.054-0.0540.0000.0000.0000.000
124A125THR0-0.051-0.03616.6770.0630.0630.0000.0000.0000.000
125A126GLU-1-0.809-0.83719.4340.3590.3590.0000.0000.0000.000
126A127GLN00.0250.00411.607-0.067-0.0670.0000.0000.0000.000
127A128ARG10.9180.98814.981-0.661-0.6610.0000.0000.0000.000
128A129SER0-0.033-0.02615.957-0.026-0.0260.0000.0000.0000.000
129A130LYS10.8280.88817.153-0.411-0.4110.0000.0000.0000.000
130A131GLY00.0460.02814.438-0.024-0.0240.0000.0000.0000.000
131A132ASP-1-0.888-0.94815.1560.6490.6490.0000.0000.0000.000
132A133ALA0-0.053-0.03017.646-0.064-0.0640.0000.0000.0000.000
133A134LEU00.0160.02114.231-0.073-0.0730.0000.0000.0000.000
134A135ASP-1-0.819-0.91713.3130.7710.7710.0000.0000.0000.000
135A136LYS10.8540.92916.761-0.323-0.3230.0000.0000.0000.000
136A137CYM-1-0.796-0.82420.4010.2260.2260.0000.0000.0000.000
137A138GLN0-0.029-0.01613.813-0.127-0.1270.0000.0000.0000.000
138A139ALA0-0.024-0.01118.888-0.049-0.0490.0000.0000.0000.000
139A140GLU-1-0.887-0.94020.2030.1850.1850.0000.0000.0000.000
140A141LEU00.0490.03821.520-0.030-0.0300.0000.0000.0000.000
141A142LYS10.9520.97717.724-0.204-0.2040.0000.0000.0000.000
142A143LYS10.8200.90222.706-0.231-0.2310.0000.0000.0000.000
143A144LEU0-0.0080.00625.497-0.014-0.0140.0000.0000.0000.000
144A145ARG10.9480.95921.933-0.067-0.0670.0000.0000.0000.000
145A146LYS10.8990.95925.251-0.141-0.1410.0000.0000.0000.000
146A147LYS10.8990.94127.880-0.090-0.0900.0000.0000.0000.000
147A148SER0-0.0020.01629.822-0.008-0.0080.0000.0000.0000.000
148A149GLN00.007-0.00531.839-0.007-0.0070.0000.0000.0000.000
149A150GLY00.0400.01633.516-0.005-0.0050.0000.0000.0000.000
150A151SER0-0.011-0.00334.4820.0040.0040.0000.0000.0000.000
151A152LYS10.9140.94737.709-0.006-0.0060.0000.0000.0000.000
152A153ASN00.0180.02832.6690.0070.0070.0000.0000.0000.000
153A154PRO00.0310.01836.869-0.002-0.0020.0000.0000.0000.000
154A155GLN00.020-0.00436.809-0.001-0.0010.0000.0000.0000.000
155A156LYS10.9580.98136.182-0.074-0.0740.0000.0000.0000.000
156A157TYR0-0.058-0.04728.9610.0070.0070.0000.0000.0000.000
157A158SER00.0410.00732.2590.0070.0070.0000.0000.0000.000
158A159ASP-1-0.794-0.89731.6900.0510.0510.0000.0000.0000.000
159A160LYS10.8360.92729.128-0.131-0.1310.0000.0000.0000.000
160A161GLU-1-0.796-0.88026.7580.0650.0650.0000.0000.0000.000
161A162LEU00.0150.00726.9370.0080.0080.0000.0000.0000.000
162A163GLN00.0590.04127.5980.0130.0130.0000.0000.0000.000
163A164TYR0-0.019-0.04024.3700.0010.0010.0000.0000.0000.000
164A165ILE0-0.004-0.00223.0020.0180.0180.0000.0000.0000.000
165A166ASP-1-0.879-0.92722.9270.1220.1220.0000.0000.0000.000
166A167ALA00.0080.00923.8610.0140.0140.0000.0000.0000.000
167A168ILE0-0.056-0.03817.9730.0310.0310.0000.0000.0000.000
168A169SER00.005-0.00419.2090.0210.0210.0000.0000.0000.000
169A170ASN0-0.039-0.02120.0160.0070.0070.0000.0000.0000.000
170A171LYS10.7940.82419.264-0.288-0.2880.0000.0000.0000.000
171A172GLN0-0.045-0.02613.9830.0460.0460.0000.0000.0000.000
172A173GLY00.0440.02715.9790.0360.0360.0000.0000.0000.000
173A174GLU-1-0.860-0.91617.9710.3080.3080.0000.0000.0000.000
174A175LEU0-0.045-0.00712.6260.0210.0210.0000.0000.0000.000
175A176GLU-1-0.800-0.86711.2930.3510.3510.0000.0000.0000.000
176A177ASN0-0.055-0.03713.942-0.024-0.0240.0000.0000.0000.000
177A178TYR0-0.069-0.05116.708-0.003-0.0030.0000.0000.0000.000
178A179VAL0-0.0080.00010.785-0.011-0.0110.0000.0000.0000.000
179A180SER0-0.009-0.00614.183-0.037-0.0370.0000.0000.0000.000
180A181ASP-1-0.824-0.89714.9500.1810.1810.0000.0000.0000.000
181A182GLY00.0420.02717.199-0.031-0.0310.0000.0000.0000.000
182A183TYR00.0080.00113.475-0.041-0.0410.0000.0000.0000.000
183A184LYS10.8460.90615.718-0.245-0.2450.0000.0000.0000.000
184A185THR0-0.022-0.01318.782-0.045-0.0450.0000.0000.0000.000
185A186ALA00.0080.00617.297-0.027-0.0270.0000.0000.0000.000
186A187LEU00.0300.01316.409-0.032-0.0320.0000.0000.0000.000
187A188THR0-0.059-0.03619.846-0.042-0.0420.0000.0000.0000.000
188A189GLU-1-0.850-0.88922.1940.1880.1880.0000.0000.0000.000
189A190GLU-1-0.901-0.95019.4450.1630.1630.0000.0000.0000.000
190A191ARG10.9660.98223.055-0.079-0.0790.0000.0000.0000.000
191A192ARG10.8600.90025.072-0.185-0.1850.0000.0000.0000.000
192A193ARG10.7370.81525.944-0.201-0.2010.0000.0000.0000.000
193A194PHE00.0210.00223.277-0.013-0.0130.0000.0000.0000.000
194A195CYS0-0.107-0.05528.411-0.014-0.0140.0000.0000.0000.000
195A196PHE00.0600.02430.786-0.007-0.0070.0000.0000.0000.000
196A197LEU00.0010.00631.015-0.005-0.0050.0000.0000.0000.000
197A198VAL00.0090.00431.850-0.007-0.0070.0000.0000.0000.000
198A199GLU-1-0.846-0.91633.8570.0640.0640.0000.0000.0000.000
199A200LYS10.8630.91736.833-0.060-0.0600.0000.0000.0000.000
200A201GLN00.0180.01737.006-0.003-0.0030.0000.0000.0000.000
201A202CYS0-0.050-0.03437.487-0.006-0.0060.0000.0000.0000.000
202A203ALA0-0.0190.00040.360-0.003-0.0030.0000.0000.0000.000
203A204VAL00.0300.02342.279-0.003-0.0030.0000.0000.0000.000
204A205ALA00.0020.00442.248-0.003-0.0030.0000.0000.0000.000
205A206LYS10.9610.98144.191-0.030-0.0300.0000.0000.0000.000
206A207ASN0-0.027-0.02246.329-0.003-0.0030.0000.0000.0000.000
207A208SER00.0230.00446.915-0.002-0.0020.0000.0000.0000.000
208A209ALA0-0.0070.00647.875-0.002-0.0020.0000.0000.0000.000
209A210ALA0-0.006-0.00249.706-0.002-0.0020.0000.0000.0000.000
210A211TYR00.0130.01051.505-0.001-0.0010.0000.0000.0000.000
211A212HIS0-0.013-0.01749.590-0.002-0.0020.0000.0000.0000.000
212A213SER0-0.029-0.01253.670-0.002-0.0020.0000.0000.0000.000
213A214LYS10.8310.90455.376-0.013-0.0130.0000.0000.0000.000
214A215GLY00.0430.01457.173-0.001-0.0010.0000.0000.0000.000
215A216LYS10.9430.96455.924-0.002-0.0020.0000.0000.0000.000
216A217GLU-1-0.855-0.90658.9880.0090.0090.0000.0000.0000.000
217A218LEU00.005-0.00361.445-0.001-0.0010.0000.0000.0000.000
218A219LEU00.0120.01060.3250.0000.0000.0000.0000.0000.000
219A220ALA0-0.029-0.01762.562-0.001-0.0010.0000.0000.0000.000
220A221GLN0-0.029-0.01464.4750.0000.0000.0000.0000.0000.000
221A222LYS10.8680.93167.134-0.008-0.0080.0000.0000.0000.000
222A223LEU00.0420.03365.1300.0000.0000.0000.0000.0000.000
223A224PRO0-0.007-0.01267.7380.0000.0000.0000.0000.0000.000
224A225LEU00.0320.01970.8060.0000.0000.0000.0000.0000.000
225A226TRP00.022-0.00366.6360.0000.0000.0000.0000.0000.000
226A227GLN0-0.0070.00369.8150.0000.0000.0000.0000.0000.000
227A228GLN0-0.009-0.01273.2000.0000.0000.0000.0000.0000.000
228A229GLY00.0100.01576.0560.0000.0000.0000.0000.0000.000
229A230VAL0-0.074-0.04073.6880.0000.0000.0000.0000.0000.000
230A231ASP-1-0.957-0.97176.9130.0000.0000.0000.0000.0000.000
231A232SER0-0.104-0.03978.7470.0000.0000.0000.0000.0000.000